PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads.

BackgroundWe introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to their data (e.g., the maximum allowed nucleosome overlap or legal ranges for the fragment sizes) our algorithm can accurately determine a genome-wide set of non-overlapping nucleosomes without any user-defined parameter. This feature makes PuFFIN significantly easier to use and prevents users from choosing the "wrong" parameters and obtain sub-optimal nucleosome maps.ResultsPuFFIN builds genome-wide nucleosome maps using a multi-scale (or multi-resolution) approach. Our algorithm relies on a set of nucleosome "landscape" functions at different resolution levels: each function represents the likelihood of each genomic location to be occupied by a nucleosome for a particular value of the smoothing parameter. After a set of candidate nucleosomes is computed for each function, PuFFIN produces a consensus set that satisfies non-overlapping constraints and maximizes the number of nucleosomes.ConclusionsWe report comprehensive experimental results that compares PuFFIN with recently published tools (NOrMAL, TEMPLATE FILTERING, and NucPosSimulator) on several synthetic datasets as well as real data for S. cerevisiae and P. falciparum. Experimental results show that our approach produces more accurate nucleosome maps with a higher number of non-overlapping nucleosomes than other tools

Coherent population trapping of a single nuclear spin under ambient conditions

Coherent control of quantum systems has far-reaching implications in quantum engineering. In this context, coherent population trapping (CPT) involving dark resonances has played a prominent role, leading to a wealth of major applications including laser cooling of atoms and molecules, optical magnetometry, light storage and highly precise atomic clocks. Extending CPT methods to individual solid-state quantum systems has been only achieved in cryogenic environments for electron spin impurities and superconducting circuits. Here, we demonstrate efficient CPT of a single nuclear spin in a room temperature solid. To this end, we make use of a three-level system with a $\Lambda$-configuration in the microwave domain, which consists of nuclear spin states addressed through their hyperfine coupling to the electron spin of a single nitrogen-vacancy defect in diamond. Dark state pumping requires a relaxation mechanism which, in atomic systems, is simply provided by spontaneous emission. In this work, the relaxation process is externally controlled through incoherent optical pumping and separated in time from consecutive coherent microwave excitations of the nuclear spin $\Lambda$-system. Such a pumping scheme with controlled relaxation allows us (i) to monitor the sequential accumulation of population into the dark state and (ii) to reach a new regime of CPT dynamics for which periodic arrays of dark resonances can be observed, owing to multiple constructive interferences. This work offers new prospects for quantum state preparation, information storage in hybrid quantum systems and metrology.Comment: 13 pages including supplementary information, links to figures correcte

Propagating Polaritons in III-Nitride Slab Waveguides

We report on III-nitride waveguides with c-plane GaN/AlGaN quantum wells in the strong light-matter coupling regime supporting propagating polaritons. They feature a normal mode splitting as large as 60 meV at low temperatures thanks to the large overlap between the optical mode and the active region, a polariton decay length up to 100 $\mu$m for photon-like polaritons and lifetime of 1-2 ps; with the latter values being essentially limited by residual absorption occurring in the waveguide. The fully lattice-matched nature of the structure allows for very low disorder and high in-plane homogeneity; an important asset for the realization of polaritonic integrated circuits that could support nonlinear polariton wavepackets up to room temperature thanks to the large exciton binding energy of 40 meV

The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum.

BackgroundGene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional control of gene expression, while at least part of Plasmodium's genome is controlled by post-transcriptional mechanisms. To generate insights into the mechanisms that regulate gene expression at the post-transcriptional level, we undertook complementary computational, comparative genomics, and experimental approaches to identify and characterize mRNA-binding proteins (mRBPs) in P. falciparum.ResultsClose to 1000 RNA-binding proteins are identified by hidden Markov model searches, of which mRBPs encompass a relatively large proportion of the parasite proteome as compared to other eukaryotes. Several abundant mRNA-binding domains are enriched in apicomplexan parasites, while strong depletion of mRNA-binding domains involved in RNA degradation is observed. Next, we experimentally capture 199 proteins that interact with mRNA during the blood stages, 64 of which with high confidence. These captured mRBPs show a significant overlap with the in silico identified candidate RBPs (p < 0.0001). Among the experimentally validated mRBPs are many known translational regulators active in other stages of the parasite's life cycle, such as DOZI, CITH, PfCELF2, Musashi, and PfAlba1-4. Finally, we also detect several proteins with an RNA-binding domain abundant in Apicomplexans (RAP domain) that is almost exclusively found in apicomplexan parasites.ConclusionsCollectively, our results provide the most complete comparative genomics and experimental analysis of mRBPs in P. falciparum. A better understanding of these regulatory proteins will not only give insight into the intricate parasite life cycle but may also provide targets for novel therapeutic strategies

Development of a Reference Wafer for On-Wafer Testing of Extreme Impedance Devices

This paper describes the design, fabrication, and testing of an on-wafer substrate that has been developed specifically for measuring extreme impedance devices using an on-wafer probe station. Such devices include carbon nano-tubes (CNTs) and structures based on graphene which possess impedances in the κ Ω range and are generally realised on the nano-scale rather than the micro-scale that is used for conventional on-wafer measurement. These impedances are far removed from the conventional 50- reference impedance of the test equipment. The on-wafer substrate includes methods for transforming from the micro-scale towards the nano-scale and reference standards to enable calibrations for extreme impedance devices. The paper includes typical results obtained from the designed wafer

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features.

Empirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism's complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture in Plasmodium transcriptional regulation and suggest that AP2 transcription factors may play a limited regulatory role, perhaps operating in conjunction with epigenetic factors

Generating Entangled Microwave Radiation Over Two Transmission Lines

Using a superconducting circuit, the Josephson mixer, we demonstrate the first experimental realization of spatially separated two-mode squeezed states of microwave light. Driven by a pump tone, a first Josephson mixer generates, out of quantum vacuum, a pair of entangled fields at different frequencies on separate transmission lines. A second mixer, driven by a $\pi$-phase shifted copy of the first pump tone, recombines and disentangles the two fields. The resulting output noise level is measured to be lower than for vacuum state at the input of the second mixer, an unambiguous proof of entanglement. Moreover, the output noise level provides a direct, quantitative measure of entanglement, leading here to the demonstration of 6 Mebit.s$^{-1}$ (Mega entangled bits per second) generated by the first mixer.Comment: 5 pages, 4 figures. Supplementary Information can be found here as an ancillary fil

Different methods of evaluation of Monilinia laxa on apricot flowers and branches

- Organic apricot production is currently not profitable. - The main obstacle to sustainable profitability is brown rot caused by the fungus Monilinia laxa (Aderh. & Ruhl). - In the current apricot germplasm no source of total resistance has been shown, but some varieties are expressing interesting levels of tolerance. - A good evaluation of the M. laxa symptoms is essential for a precise diagnosis of the infection and to appreciate differences between tolerant and susceptible varieties and genotypes

Spin-Polarized Electrons in Monolayer MoS2_2

The optical susceptibility is a local, minimally-invasive and spin-selective probe of the ground state of a two-dimensional electron gas. We apply this probe to a gated monolayer of MoS$_2$. We demonstrate that the electrons are spin polarized. Of the four available bands, only two are occupied. These two bands have the same spin but different valley quantum numbers. We argue that strong Coulomb interactions are a key aspect of this spontaneous symmetry breaking. The Bohr radius is so small that even electrons located far apart in phase space interact, facilitating exchange couplings to align the spins